bims-auttor 2025-07-13 papers

bims-auttor

Biomed News

on Autophagy and mTOR

Issue of 2025–07–13
twenty-six papers selected by
Viktor Korolchuk, Newcastle University

Modulation of mitochondrial quality control through autophagic pathway in familial Alzheimer's disease.
Hypoxia: A Raptor mutant survives in thin air.
Mutant α-synuclein takes down autophagy.
ATG16L1 membrane recruitment in autophagy.
The Fragile Balance: Autophagy's Role in Neurodegenerative Disease Progression.
Autophagic stress activates distinct compensatory secretory pathways in neurons.
Activation of endogenous PRKN by structural derepression is linked to increased turnover of the E3 ubiquitin ligase.
Evolution of growth factor signaling to the TSC complex to regulate mTORC1.
Time-restricted feeding and autophagic flux: a promising strategy for enhancing human longevity?
PINK1 Loss of Function Selectively Alters the Mitochondrial-Derived Vesicle Pathway.
Rapamycin for longevity: the pros, the cons, and future perspectives.
Deleterious Sequestosome 1 mutations G262R and P438L in amyotrophic lateral sclerosis cause autophagy and oxidative stress imbalance.
Nuclear p62/SQSTM1 facilitates ubiquitin-independent proteasomal degradation of BMAL1.
An Unstable ATG2A Variant Causes a Neurodegenerative Disorder via Impaired Autophagy and Proteotoxic Stress in Brain Atrophy.
Single-cell transcriptome atlas reveals mitophagy dynamics in acute chemical injury model and the role of MSCs transplantation.
The ESCRT protein CHMP5 restricts bone formation by controlling endolysosome-mitochondrion-mediated cell senescence.
Investigating the function of UVRAG protein in regulation of apoptosis and autophagy and its implications in cancer.
Loss of ATG5 expression in a subset of human prostate cancers promotes tumor growth through accumulation of p62.
The molecular logic of Gtr1/2- and Pib2-dependent TORC1 regulation in budding yeast.
Sensing of extracellular l-proline availability by the integrated stress response determines the outcome of cell competition.
Role of autophagy in neurotoxic protein's clearance following post-ischemic stroke: where we are and what we know?
Targeting PINK1 using phytochemicals: Exploring molecular insights into Parkinson's disease therapeutics.
Homocysteine interferes with Ndufa1 leading to mitochondrial dysfunction through repression of the NAD+/Sirt1 pathway in the brain: a possible link between hyperhomocysteinemia and neurodegeneration.
Caloric restriction mimetics chlorogenic acid and fisetin as potential autophagy inducers targeting ATG101.
PIP4K2C inhibition reverses autophagic flux impairment induced by SARS-CoV-2.
Ulk1(S555) inhibition alters nutrient stress response by prioritizing amino acid metabolism.

Biochim Biophys Acta Mol Cell Res. 2025 Jul 07. pii: S0167-4889(25)00124-7. [Epub ahead of print] 120019

Modulation of mitochondrial quality control through autophagic pathway in familial Alzheimer's disease.

Adriana Limone, Clelia Di Napoli, Giusy De Rosa, Silvia Bagnoli, Antonella Izzo, Claudio Procaccini, Giuseppe Matarese, Benedetta Nacmias, Antonio Lavecchia, Daniela Sarnataro.

  Autophagy is a highly conserved cellular catabolic process recognized as an essential pathway for the maintenance of cellular homeostasis. Growing evidence implicates autophagic dysfunction in the pathogenesis of several neurodegenerative disorders, including Alzheimer's disease (AD), thus its modulation might represent an interesting therapeutic tool. Searching for a compound that stimulates autophagic pathway, led us to identify the inhibitor of RPSA receptor, NSC47924. In this study, we show that, NSC47924 down-modulated Akt-mTOR-axis pathway, the master regulator of autophagy, which was abnormally hyperactivated in fibroblasts from genetic AD-affected patients. Consistently, by monitoring the conversion of LC3, we found that inhibition of RPSA enhanced and restored the compromised autophagic flux. Moreover, by qRT-PCR analysis we found that inhibitor treatment upregulated the expression of autophagy-linked genes. Importantly, AD-affected fibroblasts exhibited massive mitochondrial network fragmentation and mitophagy defects, which were restored through the stimulation of autophagy induced by RPSA inhibition. Consistent with an efficient elimination of dysfunctional mitochondria, we found that the turnover of both the mitophagy regulators PINK1 and Parkin and the autophagic receptors p62, NDP52, OPTN, was modulated, thus restoring a highly interconnected organelle's network. In addition, the improvement of mitochondrial morphology correlated with a functional recovery, as assessed by Seahorse analysis and mitochondrial ROS production evaluation. Collectively, our findings suggest that RPSA inhibition stimulates an autophagic pathway promoting the efficient removal of damaged mitochondria, favouring the recovery of cellular homeostasis, and counteracting crucial AD pathogenic mechanisms.

Keywords:  37/67 kDa non-integrin laminin receptor; APP V717I mutant; Alzheimer's disease; Autophagy; Mitophagy; PS1 M146L mutant; RPSA

DOI:  https://doi.org/10.1016/j.bbamcr.2025.120019
Curr Biol. 2025 Jul 07. pii: S0960-9822(25)00657-8. [Epub ahead of print]35(13): R662-R664

Hypoxia: A Raptor mutant survives in thin air.

David J Reiner.

A recent study in Caenorhabditis elegans has identified a temperature-sensitive mutation in the mTORC1 component Raptor that confers hypoxia resistance and is associated with reduced protein synthesis but not increased autophagy. These findings point to mTORC1 as a promising target in hypoxia-related conditions.

DOI: https://doi.org/10.1016/j.cub.2025.05.041
Sci Signal. 2025 Jul 08. 18(894): eaea2255

Mutant α-synuclein takes down autophagy.

Leslie K Ferrarelli.

Parkinson's disease-associated α-synuclein impairs autophagy by hijacking the cell's acetylation machinery.

DOI: https://doi.org/10.1126/scisignal.aea2255
Crit Rev Biochem Mol Biol. 2025 Jul 11. 1-16

ATG16L1 membrane recruitment in autophagy.

Fujing Wei, Nan Qin, Yunling Chen, Zhenzhen Liu, Xiaozhu Zhao, Xiaoying Yu, Ziling Feng, Yu Wang, Aimin Yang, Hongjuan Cui.

  Autophagy, a highly conserved catabolic pathway in eukaryotes, is essential for cellular survival during starvation and for maintaining cellular homeostasis. Central to autophagy is the de novo formation of double-membrane autophagosomes, which requires the orchestrated action of a set of autophagy-related (ATG) proteins. ATG16L1 is a core autophagy protein involved in distinct phases of autophagosome biogenesis, including membrane remodeling and the formation of phagophore-like membrane cups. It interacts with the ATG12-ATG5 conjugate to form the ATG12-ATG5-ATG16L1 complex, which functions as an E3-like enzyme to catalyze LC3 lipidation. The membrane targeting of the ATG12-ATG5-ATG16L1 complex is crucial for regulating autophagy and preventing ectopic membrane engagement. In this review, we summarize and discuss the potential mechanisms underlying ATG16L1 membrane recruitment, focusing on its intrinsic membrane-binding properties and partner-mediated recruitment pathways. We critically explore how these multiple mechanisms collectively ensure the proper localization and function of ATG16L1, thereby regulating the initiation of autophagy, LC3 lipidation, and the sequestration of bacteria during xenophagy.

Keywords:  ATG12–ATG5-ATG16L1 complex; ATG16L1; Autophagy; autophagosome; membrane targeting

DOI:  https://doi.org/10.1080/10409238.2025.2521321
Curr Neuropharmacol. 2025 Jul 03.

The Fragile Balance: Autophagy's Role in Neurodegenerative Disease Progression.

Bharat Bhushan, Meenakshi Dhanawat, Garima, Kashish Wilson, Sumeet Gupta, Samrat Chauhan.

  Autophagy relates to the mechanism underlying the intracellular constituents' breakdown by lysosomes. Autophagy plays an essential role in preserving and regulating cellular homeostasis by mediating the degradation of intracellular components and recycling their decomposition products. It was demonstrated that autophagy operates in-vivo in the starving reaction, initial growth, internal control of quality, and cell division. Autophagy malfunction is perhaps connected with cancer and neurological conditions, as demonstrated by current research. In conjunction with the identification of specific mutations associated with autophagy-related disorders and deeper knowledge of the pathophysiology of disorders caused by aberrant disintegration of particular autophagy substrates, autophagy activation serves a vital part in prolonging lifespans and suppressing the process of aging. To safeguard the homeostasis within a cell, cells have developed sophisticated quality-control procedures for organelles and proteins. These quality-control mechanisms maintain cellular integrity through degradation by the autophagy-lysosome or ubiquitin-proteasome systems, as well as through protein folding assistance (or refolding of misfolded proteins) provided by molecular chaperones. A great deal of neurodegenerative illnesses are indicated by the development of intracellular inclusions formed from misfolded proteins, which are believed to be an outcome of defective autophagy. Additionally, it was recently discovered that neurodegenerative illnesses are also linked with mutations in key autophagy-related genes. However, pathogenic proteins like α-synuclein and amyloid β cause damage to the autophagy system. This paper examines the recent advancements in our understanding of the link between autophagic abnormalities and the development of neurological disorders, and proposes that activating autophagy could serve as a potential therapeutic strategy.

Keywords:  Autophagy; autophagy-related gene; cancer; heart disease; liver disease; neurodegenerative disease.; protein aggregates

DOI:  https://doi.org/10.2174/011570159X377552250627113915
Proc Natl Acad Sci U S A. 2025 Jul 15. 122(28): e2421886122

Autophagic stress activates distinct compensatory secretory pathways in neurons.

Sierra D Palumbos, Jacob Popolow, Juliet Goldsmith, Erika L F Holzbaur.

  Autophagic dysfunction is a hallmark of neurodegenerative disease, leaving neurons vulnerable to the accumulation of damaged organelles and aggregated proteins. However, the late onset of diseases suggests that compensatory quality control mechanisms may be engaged to delay these deleterious effects. Neurons expressing common familial Parkinson's disease-associated mutations in the leucine-rich repeat kinase 2 (LRRK2) exhibit defective autophagy. Here, we demonstrate that both primary murine neurons and human induced Pluripotent Stem Cells (iPSC)-derived neurons harboring pathogenic LRRK2 upregulate the secretion of extracellular vesicles. We used unbiased proteomics to characterize the secretome of LRRK2G2019S neurons and found that autophagic cargos including mitochondrial proteins were enriched. Based on these observations, we hypothesize that autophagosomes are rerouted toward secretion when cell-autonomous degradation is compromised to mediate clearance of undegraded cellular waste. Immunoblotting confirmed the release of autophagic cargos and live-cell imaging demonstrated that secretory autophagy is upregulated in LRRK2G2019S neurons. We also found that LRRK2G2019S neurons upregulate the release of exosomes containing microRNAs. Live-cell imaging confirmed that this upregulation of exosomal release is dependent on hyperactive LRRK2 activity, while pharmacological experiments indicate that this release staves off apoptosis. Finally, we show that markers of both vesicle populations are upregulated in plasma from mice expressing pathogenic LRRK2. In sum, we find that neurons expressing pathogenic LRRK2 upregulate secretory autophagy and the compensatory release of exosomes to mediate waste disposal and transcellular communication, respectively. We propose that this increased secretion contributes to the maintenance of cellular homeostasis, delaying neurodegenerative disease progression over the short term while potentially contributing to neuroinflammation over the longer term.

Keywords:  Parkinson’s disease; autophagy; neurodegeneration; secretion

DOI:  https://doi.org/10.1073/pnas.2421886122
Autophagy. 2025 Jul 07.

Activation of endogenous PRKN by structural derepression is linked to increased turnover of the E3 ubiquitin ligase.

Fabienne Fiesel, Bernardo Bustillos, Jens Watzlawik, Carol Chen, Martin Berryer, Jiazhen Zhang, Paige Boneski, Caleb Hayes, Jenny Bredenberg, Eric Deneault, Zhipeng You, Narges Abdien, Nathalia Aprahamian, Taylor Goldsmith, Zahra Baninameh, Liam Cocker, Haonan Zhang, Matthew Goldberg, Edward Fon, Jean-François Trempe, Satpal Virdee, Thomas Durcan, Wolfdieter Springer.

  Loss-of-function mutations in the PINK1 and PRKN genes are the most common cause of early-onset Parkinson disease (PD). The encoded enzymatic pair selectively identifies, labels, and targets damaged mitochondria for degradation via the macroautophagy/autophagy-lysosome system (mitophagy). This pathway is cytoprotective and efforts to activate mitophagy are pursued as therapeutic avenues to combat PD and other neurodegenerative disorders. When mitochondria are damaged, the ubiquitin kinase PINK1 accumulates and recruits PRKN from the cytosol to activate the E3 ubiquitin ligase from its auto-inhibited conformation. We have previously designed several mutations that effectively derepress the structure of PRKN and activate its enzymatic functions in vitro. However, it remained unclear how these PRKN-activating mutations would perform endogenously in cultured neurons or in vivo in the brain. Here, we gene-edited neural progenitor cells and induced pluripotent stem cells to express PRKN-activating mutations in dopaminergic cultures. All tested PRKN-activating mutations indeed enhanced the enzymatic activity of PRKN in the absence of exogenous stress, but their hyperactivity was linked to their own PINK1-dependent degradation. Strikingly, in vivo in a mouse model expressing an equivalent activating mutation, we find the same relationship between PRKN enzymatic activity and protein stability. We conclude that PRKN degradation is the consequence of its structural derepression and enzymatic activation, thus resulting only in a temporary gain of activity. Our findings imply that pharmacological activation of endogenous PRKN will lead to increased turnover and suggest that additional considerations might be necessary to achieve sustained E3 ubiquitin ligase activity for disease treatment.

Keywords:  Autophagy; PINK1; Parkin; mitophagy; parkinson’s disease

DOI:  https://doi.org/10.1080/15548627.2025.2531025
Sci Signal. 2025 Jul 08. 18(894): eadw4165

Evolution of growth factor signaling to the TSC complex to regulate mTORC1.

Kun Wang, Sophie E Lockwood, Brendan D Manning.

The mechanistic target of rapamycin (mTOR) complex 1 (mTORC1) integrates signals from factors that both stimulate (exogenous growth factors) and are essential for (intracellular nutrients and energy) cellular growth. Activation of the protein kinase mTOR within mTORC1 results in the phosphorylation of downstream substrates that collectively stimulate biomass accumulation to drive cell growth. Many upstream signals, especially growth factors, regulate mTORC1 by inducing the phosphorylation of the tuberous sclerosis complex 2 (TSC2) subunit of the TSC protein complex, a conserved brake on mTORC1 activation and its promotion of cell growth. Cryo-electron microscopy studies of the TSC protein complex have revealed that this phosphoregulation of TSC2 occurs almost exclusively on residues in loops that are outside of the evolutionarily conserved core structural elements and that did not resolve in these structures. These phosphorylation-rich unstructured loops evolved with metazoans, suggesting that the regulation of mTORC1 by diverse growth factors likely evolved with the emergence of complex body plans and diverse cell types to coordinate cell growth and metabolism within and across distinct tissues. Unlike the core structure of TSC2, these loops lack disease-associated missense mutations. These features suggest that the regulatory loops on TSC2 are more amenable to evolutionary changes that enable diverse signals to converge on the TSC protein complex to regulate mTORC1.

DOI: https://doi.org/10.1126/scisignal.adw4165
J Physiol. 2025 Jul 05.

Time-restricted feeding and autophagic flux: a promising strategy for enhancing human longevity?

Gabriela Geraldo Benzoni.



Keywords:  autophagy; caloric restriction; intermittent fasting; longevity; time‐restricted eating

DOI:  https://doi.org/10.1113/JP289282
FASEB Bioadv. 2025 Jul;7(7): e70030

PINK1 Loss of Function Selectively Alters the Mitochondrial-Derived Vesicle Pathway.

Charlotte L Collier, Colleen Ruedi, Naomi J Thorne, David A Tumbarello.

  Cell homeostasis and metabolic control require the efficient function of mitochondria and implementation of quality control pathways following damage. Cells have various discrete pathways of mitochondrial quality control (mitoQC) to maintain the healthy network. PINK1 and Parkin are two key players in mitoQC, most highly associated with the ubiquitin-dependent capture and degradation of whole mitochondria by autophagy. However, these proteins have alternative roles in repair routes directing locally damaged cargo to the lysosome, such as the mitochondrial-derived vesicle (MDV) pathway. We aimed to clarify the role of PINK1 and determine how its loss of function impacts mitochondrial dynamics and quality control. Results indicate PINK1 knockout (KO) has little impact on whole mitochondrial turnover in response to damage in SH-SY5Y cells, whereas both PINK1 and Parkin KO cells have healthy mitochondrial networks with efficient ATP production. However, TOM20 positive outer-membrane and damage-induced PDH-positive inner-membrane MDVs are elevated in PINK1 KO cells. Although, in contrast to Parkin KO, this is not due to a defect in trafficking to a LAMP1-positive compartment and may instead indicate increased damage-induced flux. In comparison, loss of Atg5-dependent mitophagy has no effect on whole mitochondrial turnover and only results in a limited elevation in inner-membrane MDVs in response to damage, indicating autophagy-independent mechanisms of whole mitochondrial turnover and a minor compensatory increase in damage-induced MDVs. Therefore, these data suggest PINK1 and Parkin are dispensable for whole mitochondrial turnover, but following their perturbation have disparate effects on the MDV pathway.

Keywords:  Parkinson's; lysosome; membrane trafficking; mitochondria; mitochondrial quality control; vesicle transport

DOI:  https://doi.org/10.1096/fba.2024-00200
Front Aging. 2025 ;6 1628187

Rapamycin for longevity: the pros, the cons, and future perspectives.

Kelley M Roark, Philip H Iffland.

  Rapamycin, an antibiotic discovered in the 1970s from Streptomyces hygroscopicus on Easter Island (Rapanui), has become a critical tool in biomedical research. Initially recognized for its potent antifungal and immunosuppressive properties, rapamycin has recently gained significant attention for anti-aging therapy and seizure treatment via mTOR pathway inhibition. The mechanistic target of the rapamycin (mTOR) pathway is an evolutionarily conserved metabolic signaling cascade that regulates cell division, growth, and survival. There is growing evidence that mTOR pathway activity accelerates aging and the development of age-related diseases including cancer, atherosclerosis, diabetes, and declining immune function. Therefore physicians and "biohackers" are using mTOR inhibition via rapamycin (and rapamycin analogs) off-label for prevention of age-related conditions despite not being widely recognized as a treatment by the broader clinical community. Currently, rapamycin (i.e., sirolimus and everolimus) is FDA approved for the prevention of transplant organ rejection and for anti-seizure therapy in Tuberous Sclerosis Complex (TSC; caused by variants in TSC1 or 2). We aim to summarize the mTOR pathway, the impact rapamycin has on the mTOR pathway, and the state of rapamycin use in the field of aging and longevity. Importantly, we will discuss the gaps in knowledge, pitfalls, and potential for the use of rapamycin to prevent aging/age-related disease and discuss the lessons learned from achieving FDA approval of evirolimus for TSC-related seizures after many years of off-label use.

Keywords:  aging; epilepsy; everolimus; mTOR; sirolimus

DOI:  https://doi.org/10.3389/fragi.2025.1628187
Neuroscience. 2025 Jul 07. pii: S0306-4522(25)00773-0. [Epub ahead of print]

Deleterious Sequestosome 1 mutations G262R and P438L in amyotrophic lateral sclerosis cause autophagy and oxidative stress imbalance.

Nidhi Singh, Dibyakanti Mishra, James Gomes.

  Amyotrophic Lateral Sclerosis (ALS) is a severe neurodegenerative disease (NDD) prevalent across the world. It is known that mutations in ALS associated genes can cause imbalances between cellular processes such as apoptosis, necroptosis, autophagy and proteasomal degradation that remove dysfunctional and aggregating proteins. Two rare missense variants namely G262R (G > A) and P438L (C > T) in Sequestosome 1 (SQSTM1), were identified by our group in a cohort of Indian ALS patients. SQSTM1 codes for p62, which is an autophagy adaptor protein involved in several signaling pathways. In this study, we investigated how these SQSTM1 mutations affect autophagy and the oxidative stress response pathway in SH-SY5Y cells through quantitative RT-PCR, immunoblotting and confocal microscopy. In addition, we examined how changes in the downstream signaling pathways alters nuclear-cytoplasmic localization of TDP-43 protein, a marker protein usually found in cytoplasmic inclusions in ALS patient tissues. We observed up-regulation of autophagy marker proteins LC3-II and ubiquitin, and down-regulation of oxidative stress marker protein Nrf2. Along with LC3-II, p-OPTN and ATG5, proteins that are also associated with autophagy were up-regulated. We also observed an increase in cytoplasmic localization of TDP-43 protein in cells expressing these p62 mutant proteins. Overall, our study provides evidence that the G262R (G > A) and P438L (C > T) mutations are deleterious through mechanisms that increase cytoplasmic localization of TDP-43, and adversely affect the autophagy and oxidative stress response pathway.

Keywords:  Amyotrophic Lateral Sclerosis; Autophagy; G262R/P438L mutations; Oxidative stress; Sequestosome 1; TDP-43

DOI:  https://doi.org/10.1016/j.neuroscience.2025.07.011
PLoS Genet. 2025 Jul 10. 21(7): e1011794

Nuclear p62/SQSTM1 facilitates ubiquitin-independent proteasomal degradation of BMAL1.

Chenliang Zhang, Quanyou Wu, Huan Zhang, RuiChen Liu, Liping Li.

Brain and muscle arnt-like protein 1(BMAL1) is a critical regulator of circadian rhythm. Although transcriptional regulation of BMAL1 has been extensively studied, the mechanisms governing the stability of BMAL1 at the protein level remain unclear. p62/SQSTM1 is a crucial factor in proteostasis regulation and is involved in both autophagy and the ubiquitin-proteasome system. We demonstrated that p62 promotes proteasomal degradation of BMAL1 within the nucleus, independent of ubiquitination. Additional molecular analyses indicated that p62 functions as a receptor for the 20S proteasome, facilitating the recruitment of BMAL1 to the 20S proteasome for degradation. This mechanism is independent of recently identified p62-driven nuclear biomolecular condensates. We also revealed that remodeling the nuclear accumulation of p62 may represent a potential strategy for targeting BMAL1 to suppress tumor cell growth. In conclusion, our findings revealed a novel mechanism by which nuclear p62 regulates BMAL1 proteostasis.

DOI: https://doi.org/10.1371/journal.pgen.1011794
Clin Genet. 2025 Jul 09.

An Unstable ATG2A Variant Causes a Neurodegenerative Disorder via Impaired Autophagy and Proteotoxic Stress in Brain Atrophy.

S Rehan Ahmad, Md Zeyaullah, Abdullah M AlShahrani, Danish Qavi, Abdelrhman A G Altijani, Mohammad Suhail Khan, Khursheed Muzammil.

  Autophagy is a critical cellular process for maintaining proteostasis and neuronal health. Disruption of this pathway is increasingly recognized in pediatric neurodegenerative disorders. Here, we study a novel previously uncharacterized homozygous and autosomal recessive missense variant, c.1372G>C (p.Gly433Ala), in the autophagy gene ATG2A, identified in a 3-year-old female proband presenting with developmental regression, seizures, cerebellar ataxia, and MRI-confirmed diffuse cerebral and cerebellar atrophy. The affected residue, Gly433, is evolutionarily conserved across eukaryotes and predicted to be structurally and functionally critical. Computational modeling and molecular dynamics simulations revealed that the G433A substitution induces local β-sheet extension, increased protein flexibility, higher aggregation propensity, and global structural destabilization. Proband-derived fibroblasts expressing ATG2A-G433A showed normal transcript and protein levels, but exhibited mislocalization of ATG2A to the cytosol, reduced colocalization with LC3B, loss of autophagosome formation, and a marked increase in protein aggregates. Proteotoxic stress was further evidenced by significant accumulation of Proteostat- and SQSTM1-positive granules. Additionally, transcript levels of unfolded protein response markers (GRP78, PERK, ATF4, and CHOP) were significantly upregulated, suggesting increased ER stress signaling. Cell cycle analysis revealed a substantial increase in cell death in proband fibroblasts. Overall, our findings identify ATG2A as a potentially novel disease gene and its G433A variant as a pathogenic substitution that disrupts autophagy and proteostasis, driving neurodegeneration via aggregation-prone misfolding and autophagy failure. This work depicts the first clinical spectrum of ATG2A-related neurodegenerative disorders and highlights the importance of autophagy maintenance in pediatric neurodevelopmental processes.

Keywords:  ATG2A; autophagy; neurodegeneration; pediatric seizure; protein aggregation

DOI:  https://doi.org/10.1111/cge.70019
Stem Cell Res Ther. 2025 Jul 06. 16(1): 350

Single-cell transcriptome atlas reveals mitophagy dynamics in acute chemical injury model and the role of MSCs transplantation.

Sang Luo, Fang Wu, Xiaojun Yang.

   BACKGROUND AND PURPOSE: Mitochondrial autophagy, also referred to as mitophagy, clears damaged mitochondria and has dual functions in disease development and liver homeostasis in response to liver pathologies. Mesenchymal stem/stromal cells (MSCs) are most commonly used to treat liver failure because they are easy to obtain and present no ethical problems. However, the molecular mechanisms by which MSCs promote liver failure progression are not fully understood. This study explored the distinct mitophagy states in hepatocytes and macrophages during MSCs therapy.
EXPERIMENTAL APPROACH: To investigate tissue-specific mitophagy in acute liver failure (ALF), we generated a single-cell transcriptome (scRNA-seq) atlas of liver tissue from healthy mice, ALF mice and human umbilical cord mesenchymal stem/stromal cell (hUC-MSC)-transplanted mice.
KEY RESULTS: The data revealed the complex cellular landscape of liver tissue during ALF progression, revealing alterations in metabolic fluxes and mitophagy activation. Through the intersection of single-cell sequencing data with mitophagy-related genes (MRGs), a total of 24 differentially expressed MRGs were identified. Gene Ontology (GO) analysis further revealed that the ubiquitinating enzyme Arih1 was significantly upregulated after MSC transplantation, whereas the mitophagy genes Bnip3L/NIX and Beciln1 were significantly downregulated in mononuclear phagocytes(MPs).
CONCLUSIONS AND IMPLICATIONS: Our research demonstrated that during the development of ALF, mitophagy within hepatocytes is suppressed, whereas in MPs, mitophagy is excessively activated. MSCs are capable of alleviating disease progression by modulating the distinct mitophagy states of cells, providing an important resource for investigating mitophagy regulation in hepatic homeostasis and disease development.

Keywords:  Liver failure; Mesenchymal stem/stromal cells; Mitophagy

DOI:  https://doi.org/10.1186/s13287-025-04491-3
Elife. 2025 Jul 07. pii: RP101984. [Epub ahead of print]13

The ESCRT protein CHMP5 restricts bone formation by controlling endolysosome-mitochondrion-mediated cell senescence.

Fan Zhang, Yuan Wang, Luyang Zhang, Chunjie Wang, Deping Chen, Haibo Liu, Ren Xu, Cole M Haynes, Jae-Hyuck Shim, Xianpeng Ge.

  The dysfunction of the cellular endolysosomal pathway, such as in lysosomal storage diseases, can cause severe musculoskeletal disorders. However, how endolysosomal dysfunction causes musculoskeletal abnormalities remains poorly understood, limiting therapeutic options. Here, we report that CHMP5, a member of the endosomal sorting complex required for transport (ESCRT)-III protein family, is essential to maintain the endolysosomal pathway and regulate bone formation in osteogenic lineage cells. Genetic ablation of Chmp5 in mouse osteogenic cells increases bone formation in vivo and in vitro. Mechanistically, Chmp5 deletion causes endolysosomal dysfunction by decreasing the VPS4A protein, and CHMP5 overexpression is sufficient to increase the VPS4A protein. Subsequently, endolysosomal dysfunction disturbs mitochondrial functions and increases mitochondrial ROS, ultimately resulting in skeletal cell senescence. Senescent skeletal cells cause abnormal bone formation by combining cell-autonomous and paracrine actions. Importantly, the elimination of senescent cells using senolytic drugs can alleviate musculoskeletal abnormalities in Chmp5 conditional knockout mice. Therefore, our results show that cell senescence represents an underpinning mechanism and a therapeutic target for musculoskeletal disorders caused by the aberrant endolysosomal pathway, such as in lysosomal storage diseases. These results also uncover the function and mechanism of CHMP5 in the regulation of cell senescence by affecting the endolysosomal-mitochondrial pathway.

Keywords:  CHMP5; bone; cell biology; cell senescence; endolysosomal pathway; medicine; mouse; musculoskeletal disease; skeletal stem cell

DOI:  https://doi.org/10.7554/eLife.101984
Int J Biol Macromol. 2025 Jul 08. pii: S0141-8130(25)06402-5. [Epub ahead of print]320(Pt 2): 145847

Investigating the function of UVRAG protein in regulation of apoptosis and autophagy and its implications in cancer.

Shiv Kumar, Manash Sarma, Ehasanullah Khan, Vikash Kumar Dubey.

  The interaction between autophagy and the apoptosis process has a substantial role in cancer development, chemoresistance, cardiological disease, and neurological disorders. UVRAG, a key autophagy regulator protein, has been associated with tumor progression and suppression via its interaction with BIF1, BAX and Beclin-1. Autophagy exhibits a dualistic role in cancer biology as emerging evidence indicates its ability to promote tumor cell survival under various stress conditions. However, the time-dependent role of (temporal) autophagy in disease progression remains poorly understood. In cardiovascular disorders, the balance between autophagy and apoptosis affects cell viability and stability of long-lived proteins, whereas in neurological disorders, it disrupts amyloid beta metabolism and exacerbates neurodegeneration. The molecular mechanism of UVRAG interaction with BAX and other genes in different cancers and their effects on apoptosis and autophagy regulation in different stress environments inside the cells remains a key area. Further, we discuss targeting selective autophagy as a potential therapeutic approach. Advancements in drug delivery systems targeting autophagy-apoptotic pathways emphasize therapeutic potential while highlighting the need for precision in modulating these intricate processes. Understanding the intricate relationship between autophagy and apoptosis mediated by UVRAG with apoptotic genes elucidates cancer pathogenesis and identifies prospective targets for novel therapies.

Keywords:  Apoptosis; Autophagy; BAX; Cell death; Cross talk; Drug discovery; UVRAG

DOI:  https://doi.org/10.1016/j.ijbiomac.2025.145847
bioRxiv. 2025 May 08. pii: 2025.05.02.651776. [Epub ahead of print]

Loss of ATG5 expression in a subset of human prostate cancers promotes tumor growth through accumulation of p62.

Daric J Wible, Wen Jess Li, Xiaozhuo Liu, Manu M Sebastian, Dean G Tang, Shawn B Bratton.

Loss-of-function mutations in autophagy-related (ATG) genes are rare in cancer. However, we report herein that ATG5 is fully deleted in ∼14% of prostate cancers (PCa), rivaling that of well-established tumor suppressor genes. ATG5 expression was downregulated at both mRNA and protein levels and was associated with poor patient survival. The DU145 PCa cell line, isolated from a brain metastasis, is entirely deficient in ATG5; and while ATG5 reintroduction restored autophagy, it dramatically inhibited tumor growth in vivo and led to near complete consumption of the multifunctional autophagy receptor/signaling protein, p62. Deletion of SQSTM1 confirmed that p62 was essential for tumor growth; and Reverse Phase Protein Array analysis revealed that p62 protein was significantly increased in prostate tumors, despite a reduction in mRNA expression. Thus, ATG5 appears to function as a novel tumor suppressor in a subset of prostate tumors and does so, at least in part, through autophagic degradation of p62.

DOI: https://doi.org/10.1101/2025.05.02.651776
Elife. 2025 Jul 07. pii: RP94628. [Epub ahead of print]13

The molecular logic of Gtr1/2- and Pib2-dependent TORC1 regulation in budding yeast.

Jacob H Cecil, Cristina M Padilla, Austin A Lipinski, Paul Langlais, Xiangxia Luo, Andrew P Capaldi.

  The Target of Rapamycin kinase Complex 1 (TORC1) regulates cell growth and metabolism in eukaryotes. Previous studies have shown that, in Saccharomyces cerevisiae, nitrogen and amino acid signals activate TORC1 via the highly conserved small GTPases, Gtr1/2, and the phosphatidylinositol 3-phosphate binding protein, Pib2. However, it was unclear if/how Gtr1/2 and Pib2 cooperate to control TORC1. Here, we report that this dual regulator system pushes TORC1 into at least three distinct signaling states: (i) a Gtr1/2 on, Pib2 on, rapid growth state in nutrient replete conditions; (ii) a Gtr1/2 inhibited, Pib2 on, adaptive/slow growth state in poor-quality growth medium; and (iii) a Gtr1/2 off, Pib2 off, quiescent state in starvation conditions. We suggest that other signaling pathways work in a similar way to drive a multilevel response via a single kinase, but the behavior has been overlooked since most studies follow signaling to a single reporter protein.

Keywords:  Gtr1/2; Pib2; S. cerevisiae; TORC1; cell biology; nutrient; protein kinase

DOI:  https://doi.org/10.7554/eLife.94628
Sci Adv. 2025 Jul 11. 11(28): eadw1883

Sensing of extracellular l-proline availability by the integrated stress response determines the outcome of cell competition.

Shruthi Krishnan, Ana Lima, Sizhe Tan, Ying Thong Low, Salvador Perez Montero, Aida Di Gregorio, Adrian Perez Barreto, Sarah Bowling, Karen Vousden, Tristan A Rodriguez.

Cell competition is a conserved fitness quality control that eliminates cells that are less fit than their neighbors. How winner cells induce the elimination of losers is poorly understood. We tackle this question by studying the onset of embryonic differentiation in mice, where cell competition eliminates 35% of embryonic cells. These loser cells have mitochondrial dysfunction, which we show causes amino acid deprivation and activation of the integrated stress response (ISR), a pathway essential for their survival. We demonstrate that l-proline is a key amino acid sensed by the ISR and that proline represses the ISR and drives their elimination. These results indicate that cell competition acts as a previously unidentified tissue-sparing mechanism, regulated by the availability of extracellular amino acids, that allows for the elimination of dysfunctional cells when amino acids are plentiful but ensures their survival in nutrient-poor environments.

DOI: https://doi.org/10.1126/sciadv.adw1883
Mol Brain. 2025 Jul 08. 18(1): 60

Role of autophagy in neurotoxic protein's clearance following post-ischemic stroke: where we are and what we know?

Sareh Kazmi, Fatemeh Farokhi-Sisakht, Samin Davoody, Gozal Bahlakeh, Fatemeh Abbaszadeh, Reza Rahbarghazi, Aliakbar Shekarchi, Mohammad Karimipour.



Keywords:  Autophagy; Ischemic stroke; Neurodegeneration; Neuroinflammation; Oxidative stress; Protein aggregates

DOI:  https://doi.org/10.1186/s13041-025-01201-1
Biochem Cell Biol. 2025 Jul 07.

Targeting PINK1 using phytochemicals: Exploring molecular insights into Parkinson's disease therapeutics.

Saranya Nallusamy, Selva Babu Selvamani, Chakkarai Sathyaseelan, Divya Selvakumar, Rashmi Panigrahi.

Parkinson's disease (PD) is one of the most commonly affecting neurodegenerative disorder prevalent in our society. The inherited autosomal recessive PD/parkinsonism occurs due to mutations in six genes including the gene for PTEN (phosphatase and tensin homologue)-induced putative kinase1 (PINK1). The pathophysiology and development of disorders associated with the mitochondria occur simultaneously with the dysregulation of PINK1. The activation/regulation of PINK1 through autophagy regulators can reduce Parkinson's disease condition. This study focused on exploring the possibility of 2062 phytochemicals as autophagy regulators. In silico docking and simulation studies are performed to identify their binding with the PINK1. Our studies highlight the phytochemicals like Proanthocyanidin A-6, Withanolide Q and pseudo-ginsenoside F11 that showed higher binding energy and stable interactions during the course of simulation. This study opens avenues for testing these compounds as positive modulators of PINK1 kinase activity using in vitro and in vivo methods and use of these compounds as phytotherapeutic for treatment of PD.

DOI: https://doi.org/10.1139/bcb-2024-0280
Cell Death Dis. 2025 Jul 07. 16(1): 499

Homocysteine interferes with Ndufa1 leading to mitochondrial dysfunction through repression of the NAD+/Sirt1 pathway in the brain: a possible link between hyperhomocysteinemia and neurodegeneration.

Gaoshang Chai, Yuming Mao, Juan Gong, Shuguang Bi, Yuqi Zhang, Jiajun Wu, Liu Yang, Tianlong Gao, Haitian Fu, Chunjing Yu, Caili Ren, Guofu Zhang, Xuming Zhu, Xin Guan, Haoting Yu, Caijing Tang, Yunjuan Nie, Haitao Yu.

Mitochondrial defects are early pathological changes in neurodegenerative disease (ND). Homocysteine (Hcy) is an independent risk factor for ND. However, whether and how Hcy induces mitochondrial defects during the process of neurodegeneration is unclear. Here, we revealed that Hcy interfered with mitochondrial oxidative phosphorylation (OXPHOS) by inhibiting the mitochondrial electron transport chain (ETC) complex I, resulting in increased levels of reactive oxygen species (ROS) in the hippocampus of rats. Specifically, Hcy suppressed Ndufa1 expression, which is essential for complex I assembly and activation, by interfering with its transcription factor Creb1. Moreover, we found that Hcy induced neurodegeneration-like pathological changes in mitochondria in the brain via the inhibition of the NAD+/Sirt1 pathway, including defects in mitochondrial morphology, mitochondrial biogenesis, and mitophagy, ultimately leading to impairments in synapses and cognition, all of which were reversed by Ndufa1 upregulation. Thus, Ndufa1 is a key molecular switch of Hcy-induced mitochondrial damage, and appropriately targeting Ndufa1 or NAD+ replenishment may serve as a novel therapeutic strategy for Hcy-induced neurodegeneration and cognitive impairment.

DOI: https://doi.org/10.1038/s41419-025-07834-3
Biochem Biophys Rep. 2025 Sep;43 102081

Caloric restriction mimetics chlorogenic acid and fisetin as potential autophagy inducers targeting ATG101.

Apoorv Sharma, Indu Kumari, Asimul Islam, Hridayesh Prakash, Amresh Prakash, Vijay Kumar.

  Autophagy is an important cytoprotective process impaired in neurodegenerative diseases such as Alzheimer's disease. The initiation process is mediated by the protein kinase Unc-51-like kinase 1 (ULK1) complex. ATG101, a cytosolic protein, plays a pivotal role in initiating autophagy as a component of the ULK complex in mammalian cells. It is important to understand the regulatory processes of individual autophagy components under different conditions for the development of therapeutic interventions. The caloric restriction mimetics (CRMs) such as chlorogenic acid (CGA) and fisetin mimic the healthy outcomes of caloric restriction without decreasing caloric consumption, constituting promising therapeutic candidates for neuroprotection. We explored the ATG101 interactions of CGA and fisetin in this work. Molecular docking and molecular dynamics (MD) simulations were used to investigate the interactions of these CRMs with ATG101, evaluating binding stability and dynamics. To confirm these interactions, we conducted quantitative real-time PCR (qRT-PCR) in differentiated SHSY5Y cells, analyzing the effect of CGA and fisetin on ATG101 gene expression. Our results indicated that fisetin forms a more stable complex with ATG101 compared to CGA. Yet, at the transcriptional level, both CRMs stimulate the mRNA level of ATG101. Therefore, these CRMs can be responsible for their potential as autophagy inducers. These findings offer significant insights into the molecular processes through which CRMs may improve neurodegenerative diseases by triggering autophagy.

Keywords:  ATG101; Autophagy; CRM; Gene expression; Interactions; Molecular dynamics simulation

DOI:  https://doi.org/10.1016/j.bbrep.2025.102081
Nat Commun. 2025 Jul 10. 16(1): 6397

PIP4K2C inhibition reverses autophagic flux impairment induced by SARS-CoV-2.

Marwah Karim, Manjari Mishra, Chieh-Wen Lo, Sirle Saul, Halise Busra Cagirici, Manon Gourdelier, Luca Ghita, Amrita Ojha, Do Hoang Nhu Tran, Aditi Agrawal, Connor McGraw, Michael P East, Karen Anbro Gammeltoft, Malaya Kumar Sahoo, Nancie A Mooney, Gary L Johnson, Soumita Das, Pieter Leyssen, Johan Neyts, Winston Chiu, Courtney A Cohen, Jens Bukh, Judith Gottwein, John M Dye, Norma Neff, Peter K Jackson, Benjamin A Pinsky, Tuomo Laitinen, Tatu Pantsar, Antti Poso, Fabio Zanini, Steven De Jonghe, Christopher R M Asquith, Shirit Einav.

In search for broad-spectrum antivirals, we discover a small molecule inhibitor, RMC-113, that potently suppresses the replication of multiple RNA viruses including SARS-CoV-2 in human lung organoids. We demonstrate selective inhibition of the lipid kinases PIP4K2C and PIKfyve by RMC-113 and target engagement by its clickable analog. Lipidomics analysis reveals alteration of SARS-CoV-2-induced phosphoinositide signature by RMC-113 and links its antiviral effect with functional PIP4K2C and PIKfyve inhibition. We identify PIP4K2C's roles in SARS-CoV-2 entry, RNA replication, and assembly/egress, validating it as a druggable antiviral target. Integrating proteomics, single-cell transcriptomics, and functional assays, reveals that PIP4K2C binds SARS-CoV-2 nonstructural protein 6 and regulates virus-induced autophagic flux impairment. Promoting viral protein degradation by reversing autophagic flux impairment is a mechanism of antiviral action of RMC-113. These findings reveal virus-induced autophagy regulation via PIP4K2C, an understudied kinase, and propose dual PIP4K2C and PIKfyve inhibition as a candidate strategy to combat emerging viruses.

DOI: https://doi.org/10.1038/s41467-025-61759-1
bioRxiv. 2025 Jul 04. pii: 2025.06.30.662412. [Epub ahead of print]

Ulk1(S555) inhibition alters nutrient stress response by prioritizing amino acid metabolism.

Orion S Willoughby, Anna S Nichenko, Matthew H Brisendine, Niloufar Amiri, Shelby N Henry, Daniel S Braxton, John R Brown, Kalyn S Specht, Adele K Addington, Alexey V Zaitsev, Steven T Burrows, Ryan P McMillan, Haiyan Zhang, Spencer A Tye, Charles P Najt, Siobhan M Craige, Timothy W Rhoads, Junco S Warren, Joshua C Drake.

Metabolic flexibility, the capacity to adapt fuel utilization in response to nutrient availability, is essential for maintaining energy homeostasis and preventing metabolic disease. Here, we investigate the role of Ulk1 phosphorylation at serine 555 (S555), a site regulated by AMPK, in coordinating metabolic switching following short-term caloric restriction and fasting. Using Ulk1(S555A) global knock-in mice, we show loss of S555 phosphorylation impairs glucose oxidation in skeletal muscle and liver during short-term CR, despite improved glucose tolerance. Metabolomic, transcriptomic, and mitochondrial respiration analyses reveal a compensatory reliance on glucogenic amino acids, particularly alanine and serine, in Ulk1(S555A) mice, with sustained amino acid oxidation during fasting and blunted mitochondrial response to energetic stress. These findings establish Ulk1(S555) phosphorylation as a critical regulatory event linking nutrient stress to substrate switching and highlights an underappreciated role of Ulk1 in maintaining metabolic flexibility.

DOI: https://doi.org/10.1101/2025.06.30.662412